From ef3a069ad026d31a1742dc9b860c5f545d608eaf Mon Sep 17 00:00:00 2001
From: Adam Huffman <bloch@verdurin.com>
Date: Sep 08 2011 11:11:56 +0000
Subject: Update BEDTools to 2.13.1


---

diff --git a/BEDTools.spec b/BEDTools.spec
index 39c452c..43fbb54 100644
--- a/BEDTools.spec
+++ b/BEDTools.spec
@@ -1,5 +1,5 @@
 Name:		BEDTools
-Version:	2.12.0
+Version:	2.13.1
 Release:	1%{?dist}
 Summary:	A flexible suite of utilities for comparing genomic features
 
@@ -9,7 +9,7 @@ URL:		http://code.google.com/p/bedtools/
 
 # Download is listed in an RPM-unfriendly way on the Google Code site
 # The file can be obtained at
-# http://bedtools.googlecode.com/files/BEDTools.v2.12.0.tar.gz
+# http://bedtools.googlecode.com/files/BEDTools.v2.13.0.tar.gz
 
 Source0:	http://bedtools.googlecode.com/files/%{name}.v%{version}.tar.gz
 Source1:	http://bedtools.googlecode.com/files/%{name}-User-Manual.v4.pdf
@@ -80,15 +80,17 @@ rm -rf %{buildroot}
 %{_bindir}/closestBed
 %{_bindir}/complementBed
 %{_bindir}/coverageBed
-%{_bindir}/cuffToTrans
+#%{_bindir}/cuffToTrans
 %{_bindir}/fastaFromBed
-%{_bindir}/fjoin
+#%{_bindir}/fjoin
 %{_bindir}/flankBed
 %{_bindir}/genomeCoverageBed
 %{_bindir}/intersectBed
 %{_bindir}/linksBed
 %{_bindir}/maskFastaFromBed
 %{_bindir}/mergeBed
+%{_bindir}/multiBamCov
+%{_bindir}/nucBed
 %{_bindir}/overlap
 %{_bindir}/pairToBed
 %{_bindir}/pairToPair
@@ -96,6 +98,7 @@ rm -rf %{buildroot}
 %{_bindir}/slopBed
 %{_bindir}/sortBed
 %{_bindir}/subtractBed
+%{_bindir}/tagBam
 %{_bindir}/unionBedGraphs
 %{_bindir}/windowBed
 
@@ -107,6 +110,13 @@ rm -rf %{buildroot}
 %doc %{name}-User-Manual.v4.pdf
 
 %changelog
+* Thu Sep  8 2011 Adam Huffman <bloch@verdurin.com> - 2.13.1-1
+- new upstream minor release including fixes for tagBam
+
+* Tue Sep  6 2011 Adam Huffman <bloch@verdurin.com> - 2.13.0-1
+- new upstream release 2.13.0
+- new tools tagBam and nucBed
+
 * Tue Apr 12 2011 Adam Huffman <bloch@verdurin.com> - 2.12.0-1
 - new upstream release 2.12.0
 - new tools cuffToTrans and flankBed